Genome-Wide Survey and Analysis of Microsatellite Sequences in Bovid Species

Abstract

Microsatellites or simple sequence repeats (SSRs) have become the most popular source of genetic markers, which are ubiquitously distributed in many eukaryotic and prokaryotic genomes. This is the first study examining and comparing SSRs in completely sequenced genomes of the Bovidae. We analyzed and compared the number of SSRs, relative abundance, relative density, guanine-cytosine (GC) content and proportion of SSRs in six taxonomically different bovid species: Bos taurus, Bubalus bubalis, Bos mutus, Ovis aries, Capra hircus, and Pantholops hodgsonii. Our analysis revealed that, based on our search criteria, the total number of perfect SSRs found ranged from 663,079 to 806,907 and covered from 0.44% to 0.48% of the bovid genomes. Relative abundance and density of SSRs in these Bovinae genomes were non-significantly correlated with genome size (Pearson, r < 0.420, p > 0.05). Perfect mononucleotide SSRs were the most abundant, followed by the pattern: perfect di- > tri- > penta- > tetra- > hexanucleotide SSRs. Generally, the number of SSRs, relative abundance, and relative density of SSRs decreased as the motif repeat length increased in each species of Bovidae. The most GC-content was in trinucleotide SSRs and the least was in the mononucleotide SSRs in the six bovid genomes. The GC-contents of tri- and pentanucleotide SSRs showed a great deal of similarity among different chromosomes of B. taurus, O. aries, and C. hircus. SSR number of all chromosomes in the B. taurus, O.aries, and C. hircus is closely positively correlated with chromosome sequence size (Pearson, r > 0.980, p < 0.01) and significantly negatively correlated with GC-content (Pearson, r < -0.638, p < 0.01). Relative abundance and density of SSRs in all chromosomes of the three species were significantly negatively correlated with GC-content (Pearson, r < -0.333, P < 0.05) but not significantly correlated with chromosome sequence size (Pearson, r < -0.185, P > 0.05). Relative abundances of the same nucleotide SSR type showed great similarity among different chromosomes of B. taurus, O. aries, and C. hircus.

Comparative analyses of simple sequence repeats (SSRs) in 23 mosquito species genomes: Identification, characterization and distribution (Diptera: Culicidae)

“…A, R 2 = 0.8992, P < 0.01). This phenomenon was the same as that for 30 marine species reported (Jiang et al ., ) and six bovid species (Qi et al ., ), in which the genome sizes were also correlated with the SSR numbers. SSRs are supposed to contribute to larger genome sizes since the accumulation of genes is not responsible for large differences in genome size (Jiang et al ., ).…”

“…Whole‐genome SSR detection has been reported in plants such as Oryza minuta and Or. punctata (Wang et al ., ), Sesamum indicum (Wei et al ., ), and Ziziphus jujuba (Xiao et al ., ) and in 30 marine animals (Jiang et al ., ), six species of birds (Huang et al ., ), six species of bovids (Qi et al ., ), Apis cerana (Liu et al ., ) and Tribolium castaneum (Demuth et al ., ). The SSRs in coding sequences (CDs) of 25 insect species have been identified and comparatively analyzed (Behura & Severson, ).…”

Distinct patterns of simple sequence repeats and GC distribution in intragenic and intergenic regions of primate genomes

“…In the bovid genomes, mononucleotides SSRs were also the most abundant repeat type, accounting for 43.01% – 45.33% of all SSRs, followed by the pattern: di- > tri- > Penta- > tetra- > hexanucleotides SSRs. It has been reported that the abundance of mononucleotide SSRs are more than other nucleotide SSRs in eukaryotic genomes [26,27]. Also, mononucleotide SSRs are the most abundance in all human chromosomes [28].…”

“…The intergenic regions referred to the interval sequences between gene and gene that were not included the introns, CDSs, UTRs, and other sequences. SSRs can be grouped into six categories [26,61,62], which were identified and scanned for SSRs of 1-6 bp using the software MSDB (Microsatellite Search and Building Database) downloaded at https://code.google.com/p/msdb/ [63]. To compare our results, we performed a similar analysis of these primate genomes using the same bioinformatics tool and search parameters.…”

“…In this study, repeats with unit patterns being circular permutations and/or reverse complements of each other were grouped together as one type for statistical analysis [64,65]. For tetra- and hexanucleotide repeats, combinations representing perfect di- and tri-nucleotide repeats were filtered from the final counts [26]. The combinations of SSRs for this study will help to a better knowledge of total SSRs occurrence, and their genomic locations will be very useful in selecting SSRs representative of similar repeat classes from different genomic regions as potential markers.…”